I think I see what is going on. I was measuring based on the fretboard meeting the body at the 14th fret.
I placed the nut on the neck per the instructions, then the fretboard, and then measured. This moved the bridge back enough so that I can bring the x-brace/bridge plate forward about 1/16" and have the bridge plate right under the bridge and fit tightly to the x-braces.
So, do ukuleles not always have the neck meet the body at a fret like a guitar? The pics of the StewMac kit do not.
If that is the case, the plans need revised to show the proper placement of the baces and bridge plate.
Or I still haven't figured out what I'm doing wrong.
Again , don't worry about this yet.
There is usually a bit of 'wiggle room' with nut placement.
If you are willing to do a bit of fiddling, try the following :
Don't glue the fret board to neck.
Close the box.
Prepare the neck to body joint to get a neat fit to the body.
Install the dowels, as already discussed, no glue yet, it will come apart easily.
Temporarily clamp the neck to body, no glue... (longish F-clamp with padding).
Slide the fret board up the neck until the 14th fret slot is over the neck-body join (if that is what the plan recommends).
Firmly tape the fret board to the neck in this position, so that it can not move.
Place the saddle into the bridge slot.
Position the bridge so that the saddle string departure point is the distance from the string departure point of the nut to the mid point of the 12th fret slot multiplied X 2 plus ~ 2.0mm (or any other recommended/desired figure) for compensation.
Check the centre alignment of the fret board to bridge/saddle using two 24”steel rulers.
Adjust, and re-check your measurements..
Securely tape the bridge to the body at this location.
Ascertain that the bridge position is over the bridge plate. It should be.
Measure the distance from the nut string departure to the saddle string departure.
This should now be the given scale length. But it may be a little longer if SM has not included a compensation factor.
If you wish to double check this go to an online fret calculator, follow the instructions for the measured scale length minus the compensation factor, then check the progressive figure for the 12th fret. If all is well this should be the same as your 0-12 measurement.
Now, this is where the 'fudging' begins.
If the nut is a little higher up the neck than you expect, you should be able to re-profile the transition area with a small half round file and paper, without any ill effect. The aesthetics of the appearance is up to you.
I do this with necks and fret boards that I buy in (lazy, yes, I know) as some of them are made to approximate, but not always strictly standard, scale lengths. Not checking this is a mistake that you only make once.
Always check for the correct measurement of the first fret spacing as some factory manufactured fret boards have provision for an optional zero fret (with no mention of it in the specs) and have to be adjusted if that is not in your plans. These always look a bit odd, but sometimes not odd enough to ring alarm bells. Again, a mistake that you will only make once.